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1ycl

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Revision as of 08:43, 20 January 2021

Crystal Structure of B. subtilis LuxS in Complex with a Catalytic 2-Ketone Intermediate

Structural highlights

1ycl is a 1 chain structure with sequence from "vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
Gene:	luxS ("Vibrio subtilis" Ehrenberg 1835)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[LUXS_BACSU] Involved in the synthesis of autoinducer 2 (AI-2) which is secreted by bacteria and is used to communicate both the cell density and the metabolic potential of the environment. The regulation of gene expression in response to changes in cell density is called quorum sensing. Catalyzes the transformation of S-ribosylhomocysteine (RHC) to homocysteine (HC) and 4,5-dihydroxy-2,3-pentadione (DPD).[HAMAP-Rule:MF_00091]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

S-Ribosylhomocysteinase (LuxS) is an Fe(2+)-dependent metalloenzyme that catalyzes the cleavage of the thioether bond in S-ribosylhomocysteine (SRH) to produce homocysteine (Hcys) and 4,5-dihydroxy-2,3-pentanedione (DPD), the precursor of type II bacterial quorum-sensing molecule. The proposed mechanism involves an initial metal-catalyzed aldose-ketose isomerization reaction, which results in the migration of the ribose carbonyl group from its C1 to C2 position and the formation of a 2-ketone intermediate. A repetition of the isomerization reaction shifts the carbonyl group to the C3 position. Subsequent beta-elimination reaction at the C4 and C5 positions completes the catalytic cycle. In this work, a catalytically inactive mutant (C84A) of Co(2+)-substituted Bacillus subtilis LuxS was cocrystallized with the 2-ketone intermediate and the structure was determined to 1.8 A resolution. The structure reveals that the C2 carbonyl oxygen is directly coordinated with the metal ion, providing strong support for the proposed Lewis acid function of the metal ion during catalysis. Cys-84 and Glu-57 are optimally positioned to act as general acids/bases during the isomerization and elimination reactions. In addition, Ser-6, His-11, and Arg-39 are involved in substrate/ intermediate binding through hydrogen bonding interactions. The above conclusions are further confirmed by site-directed mutagenesis and visible absorption spectroscopic studies.

Crystal structure of S-ribosylhomocysteinase (LuxS) in complex with a catalytic 2-ketone intermediate.,Rajan R, Zhu J, Hu X, Pei D, Bell CE Biochemistry. 2005 Mar 15;44(10):3745-53. PMID:15751951^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Rajan R, Zhu J, Hu X, Pei D, Bell CE. Crystal structure of S-ribosylhomocysteinase (LuxS) in complex with a catalytic 2-ketone intermediate. Biochemistry. 2005 Mar 15;44(10):3745-53. PMID:15751951 doi:10.1021/bi0477384

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1ycl"

@@ Line 1: / Line 1: @@
 ==Crystal Structure of B. subtilis LuxS in Complex with a Catalytic 2-Ketone Intermediate==
-<StructureSection load='1ycl' size='340' side='right' caption='[[1ycl]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+<StructureSection load='1ycl' size='340' side='right'caption='[[1ycl]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1ycl]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YCL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YCL FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1ycl]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YCL OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1YCL FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=KRI:(S)-2-AMINO-4-[(2S,3R)-2,3,5-TRIHYDROXY-4-OXO-PENTYL]MERCAPTO-BUTYRIC+ACID'>KRI</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=KRI:(S)-2-AMINO-4-[(2S,3R)-2,3,5-TRIHYDROXY-4-OXO-PENTYL]MERCAPTO-BUTYRIC+ACID'>KRI</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
 <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">luxS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ycl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ycl OCA], [http://pdbe.org/1ycl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ycl RCSB], [http://www.ebi.ac.uk/pdbsum/1ycl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1ycl ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1ycl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ycl OCA], [http://pdbe.org/1ycl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ycl RCSB], [http://www.ebi.ac.uk/pdbsum/1ycl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1ycl ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 34: / Line 34: @@
 </StructureSection>
 [[Category: Vibrio subtilis ehrenberg 1835]]
+[[Category: Large Structures]]
 [[Category: Bell, C E]]
 [[Category: Hu, X]]

1ycl

From Proteopedia

Revision as of 08:43, 20 January 2021

Crystal Structure of B. subtilis LuxS in Complex with a Catalytic 2-Ketone Intermediate

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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